Recombinant minimal catalytic vanadium haloperoxidases and their uses

ABSTRACT

The present invention provides new recombinantly produced vanadium haloperoxidases. The enzymes are useful in a number of industrial applications.

This application is a division of U.S. patent application Ser. No. 09/596,794, filed Jun. 19, 2000, now U.S. Pat. No. 6,656,715. This application is also a continuation in part of U.S. patent application Ser. No. 09/151,189, filed Sep. 10, 1998, now U.S. Pat. No. 6,232,457, the disclosure of which is incorporated by reference in the entirety.

FIELD OF THE INVENTION

The present invention relates to cloning and recombinant expression of proteins. In particular, it relates to expression of vanadium haloperoxidase polypeptides.

BACKGROUND OF THE INVENTION

Vanadium haloperoxidase enzymes are useful in industrial catalysis in a variety of contexts (Sheffield, et al., Biotechnology Techniques, 8:579–582 (1994)). For instance, they catalyze a variety of halogenation, oxidation and epoxidation reactions (Itoh, et al., Eur. J. Biochem., 172:477 (1988); Itoh, et. al. Biochimica et Biophysica Acta., 1994 (1993); Itoh, et al., Appl. Microbiol. & Biotechnol., 43:394–401 (1995)). Although a halide ion is a required cofactor for enzyme activity, products may not be halogenated. Numerous uses in synthetic organic chemistry include reactions with diverse substrates such as aliphatic and aromatic hydrocarbons, phenols, β-diketones and nitrogen- and sulfur-containing heterocycles (Itoh, et al., Eur. J. Biochem. 172:477 (1988); Neidleman et al., Biohalogenation: Principles, Basic Roles and Applications, Ellis Horwood, John Wiley & Sons, New York (1986)). Bromoperoxidases can also be used in place of synthetic organic chemistry reactions to make activated intermediates or products such as pesticides. In addition, these enzymes have an advantage over chemical synthesis in producing stereospecific products (Itoh, et al., Eur. J. Biochem., 172:477 (1988)). Moreover, haloperoxidases have unusual stability (both temporal and thermal) and are active in solvents including methanol, ethanol and acetone.

Recent medical applications of bromoperoxidase have been described. Lovqvist, et al., Nuclear Medicine and Biology, 22:125–131 (1995) described the enzymatic bromination of a monoclonal antibody with BR-radionuclide for imaging of antibody localization by PET scanning. There is current interest in enzymatic production of antibiotics including fosfomycin and pyrrolnitrin (Itoh, et. al. Biochimica et Biophysica Acta. 1994 (1993); Itoh, et al., Appl. Microbiol. &Biotechnol. 43:394–401 (1995)) and 7-chlorotetracycline (van Pée, K. H., J. Bacteriol., 170:5890–5894 (1988)) via haloperoxidase-catalyzed reactions in bacteria.

Known haloperoxidases include bromoperoxidases from brown and red algae including Fucus and Ascophyllum (Butler, et al., Chem. Rev., 93:1937–1994 (1993)), iodoperoxidase from green algae (Mehrtens, G., Polar Biol. 14:351–354 (1994)), and chloroperoxidase from the fungus Curvularia inaequalis (Van Schijndel, et al., Eur. J. Biochem., 225:151–157 (1994)). A vanadate requirement for algal haloperoxidase was first described by Vilter (Vilter, H., Biological Systems, 31, Vanadium and its role in life, Sigel, et al. (Eds.), Marcel Dekker, New York, N.Y., pp. 325–362 (1995)).

The specific bromoperoxidase activity of the native Fucus enzyme is several fold higher (Butler, et al.) than the other algal enzymes for which at least partial sequences have been reported, Ascophyllum (Vilter 1995) and Corallina (Shimonishi, et al. FEBS Letters, 428, 105–110 (1998)), and higher specific activity than the Curvularia fungal chloroperoxidase (van Schijndel et al. BBA 1161:249–256 (1993)).

Extracted and partially purified bromoperoxidase from the red alga Corallina officinalis is commercially available from Sigma Chemical Company. Sigma has also investigated immobilization of enzyme on agarose beads (Sheffield, et al., Phytochemistry, 38:1103–1107 (1995)) and on cellulose acetate membrane (Sheffield, et al., Biotechnology Techniques, 8:579–582 (1994)) for repetitive catalysis of bromination reactions in flow-through reactors in enzyme-driven preparative organic chemistry. Many industrial uses for stable soybean peroxidase are envisioned by A. Pokora of Enzymol International, Inc. as described by Wick (Wick, C. B., Genetic Engineering News, 16(3):1, 18–19). Recombinant enzyme biotechnology is of current industrial interest because enzymes are safe, low-polluting alternatives to chemicals in many applications, and can be modified by protein engineering to fit the requirements of specific applications (Kelly, E. B. Genetic Engineering News, 16(5):1, 30, 32 (1996) Lovqvist, et al., Nuclear Medicine and Biology, 22:125–131 (1995)). Peroxidases can also be incorporated into moldable plastics (Service, R. F., Science 272:196–197 (1996)).

Multiple representatives of other classes of peroxidases have been produced in recombinant form. A heme peroxidase, manganese peroxidase from the fungus Phanerochaete chrysosporidium, was expressed in recombinant form and refolded for activity (Whitwam, R. E., Biochem. Biophys. Research. Communications, 216:1013–1017 (1995)). Recombinant horseradish peroxidase isozyme C (a heme peroxidase) for use in chemiluminescent labeling in molecular biology and biotechnology applications has been described (EP 0299682, WO 89/03424 ). Recombinant non-heme haloperoxidases have been prepared from the bacteria, Pseudomonas pyrrocinia (Wolfframm, et al., Gene 130:131–135 (1993)) and two related Streptomyces aureofaciens enzymes (van Pée, K. H., J. Bacteriol., 170:5890–5894 (1988); Pfeifer, et al., J. Gen. Microbiol. 138:1123–1131 (1992)).

The X-ray structure for the fungal chloroperoxidase from Curvularia has been reported Messerschmidt and Wever., Proc. Natl. Acad. Sci. U.S.A. 93:392–396 (1996). The chloroperoxidase consisted of two helical bundle domains organized as an N-terminal noncatalytic bundle and a C-terminal catalytic bundle. The X-ray structure of the bromoperoxidase from the brown alga Ascophyllum (Weyand et al J. Mol. Biol. 293:595–611 (1999)) and the bromoperoxidase from the red alga Corallina (Littlechild Curr, Opin. Chem. Biol. 3:28–34 (1999)) have been published.

Despite the interest in vanadium haloperoxidases, there are relatively few reports in the literature of the cloning and recombinant expression of a vanadium haloperoxidases. Shimonshi et al. FEBS Lett. 428:105–110 (1998) described cloning of the enzyme from Corallina pilulifera. Cloning of the Curvularia gene is described by Hemrika, et al. PNAS 94,2145–2149 (1997) and 95/27046. A partial sequence of the Ascophyllum gene is described in Vilter (1995). There is a need in the art for efficient means for producing vanadium haloperoxidases using techniques such as recombinant expression. The present invention addresses these and other needs.

SUMMARY OF THE INVENTION

The present invention provides isolated nucleic acids comprising a polynucleotide sequence encoding a vanadium haloperoxidase polypeptide consisting of a catalytic helical frame that complexes a vanadium ion and catalyzes the oxidation of o-dianisidine (ODA). The polypeptides of the invention preferably comprise amino acids unique to the Fucus haloperoxidase. Examples include an Ala residue at a position corresponding to position 455 of SEQ ID NO: 2, a Cys residue at a position corresponding to position 457 of SEQ ID NO: 2, or a Val residue at position 525 of SEQ ID NO: 2.

In some embodiments, the haloperoxidase polypeptide comprises an amino acid sequence having at least about 70% amino acid sequence identity to an amino acid sequence from residue 435 to residue 632 as set forth in SEQ ID NO:2. The polypeptide may have a molecular weight of about 20 kDa. The isolated nucleic acid will usually have a polynucleotide sequence at least about 70% sequence identity to a subsequence as of SEQ ID NO:1.

To facilitate recombinant expression, the polynucleotide sequence is often included in a recombinant expression cassette in which the polynucleotide sequence is operably linked to a promoter sequence. The invention also provides cells comprising the expression cassette of the invention.

In some embodiments, the polypeptides of the invention are immobilized on a solid surface. The polypeptide may further comprise a cleavable linker sequence, such as an enterokinase cleavable linker sequence. The polypeptide may also further comprise an purification tag, such as a plurality of histidine residues.

The invention also provides method for enzymatically halogenating or oxidizing a compound using the enzymes of the invention.

The invention further provides method for preparing active vanadium haloperoxidase polypeptides of the invention using preferred methods of refolding. The refolding may comprise contacting the vanadium haloperoxidase polypeptide with an ammonium sulfate solution with or without magnesium sulfate. In other embodiments, the method use magnesium sulfate, preferably at about 0° C. to about 10° C. Still further methods of refolding comprise contacting the vanadium haloperoxidase polypeptide with imidazole and sodium or potassium chloride, preferably at about 10° C. to about 17° C.

DEFINITIONS

A “vanadium haloperoxidase polypeptide” of the invention is an isolated protein capable of catalyzing the oxidation of o-dianisidine (ODA) when complexed with a vanadium ion. Vanadium haloperoxidases of the invention can also be identified by the presence of a catalytic frame helical motif (sometimes referred to herein as a “catalytic bundle”) exemplified by residues 435 to residue 631 in SEQ ID NO:2. The catalytic frame motif of a haloperoxidase comprises the helices immediately part of or adjacent to the three conserved vanadium-binding regions identified below. The fourth helix of the catalytic frame can be either upstream of the equivalent of α1 in the Fucus sequence (as in the fungal haloperoxidases wherein the four helical frame is composed of helices K, L, N, and O and L, N and O are associated with vanadate binding site) or equivalent to α4 in the Fucus sequence. Polypeptides of the invention typically have a sequence at least about 70% identical (as determined below), usually at least about 80% identical to the sequence from residue 435 to residue 631 in SEQ ID NO:2. One of skill will recognize that the sequence of the polypeptide can be altered without substantially altering activity of the polypeptide (e.g., by conservative substitutions). In addition, as explained below, less conservative modifications (e.g., substitutions, additions, and deletions) can be made to facilitate proper refolding, purification, and the like, as desired.

Full length vanadium haloperoxidase polypeptides of the invention typically have a mass of about 73.4 kDa, and have a sequence as shown in SEQ ID NO:2. One of skill will recognize that shorter vanadium haloperoxidase polypeptides can also be used. For instance, the polypeptides can consist essentially of the C terminal region described above. The polypeptides may thus comprise from about 90 amino acids to about 300 amino acids, or from about 120 to about 250 amino acids. Exemplary polypeptide having a mass of about 20 kDa or less are described in detail below.

A “polynucleotide sequence encoding a vanadium haloperoxidase polypeptide” of the invention is a polynucleotide which encodes a vanadium peroxidase polypeptide as described above. Thus, the nucleic acids of the invention can be altered by substitutions, deletions, and additions, as desired. Polynucleotide sequences of the invention will typically be at least about 60%, usually at least about 70%, more usually at least about 80%, and often at least about 90% or 95% identical to a subsequence of SEQ ID NO:1 which encodes 435 to residue 631 in SEQ ID NO:2. Polynucleotides of the invention can also be identified by their ability to hybridize under defined conditions to such a nucleic acid. Means for determining this are described in detail below.

A polynucleotide sequence is “heterologous to” an organism or a second polynucleotide sequence if it originates from a foreign species, or, if from the same species, is modified from its original form. For example, a promoter operably linked to a heterologous coding sequence refers to a coding sequence from a species different from that from which the promoter was derived, or, if from the same species, a coding sequence which is different from any naturally occurring allelic variants.

A polynucleotide “exogenous to” an individual organism or cell is a polynucleotide which is introduced into the organism or cell using genetic engineering techniques.

The phrase “nucleic acid sequence” refers to a single or double-stranded polymer of deoxyribonucleotide or ribonucleotide bases read from the 5′ to the 3′ end. It includes chromosomal DNA, self-replicating plasmids, infectious polymers of DNA or RNA and DNA or RNA that performs a primarily structural role.

A “promoter” is defined as an array of nucleic acid control sequences that direct transcription of an operably linked nucleic acid. Promoters include necessary nucleic acid sequences near the start site of transcription, such as, in the case of a polymerase II type promoter, a TATA element. A promoter also optionally includes distal enhancer or repressor elements, which can be located as much as several thousand base pairs from the start site of transcription. A “constitutive” promoter is a promoter that is active under most environmental and developmental conditions. An “inducible” promoter is a promoter that is active under environmental or developmental regulation. The term “operably linked” refers to a functional linkage between a nucleic acid expression control sequence (such as a promoter, or array of transcription factor binding sites) and a second nucleic acid sequence, wherein the expression control sequence directs transcription of the nucleic acid corresponding to the second sequence.

In the case where the inserted polynucleotide sequence is transcribed and translated to produce a functional polypeptide, one of skill will recognize that because of codon degeneracy a number of polynucleotide sequences will encode the same polypeptide. In addition, the term specifically includes those sequences substantially identical (determined as described below) with polynucleotide sequences disclosed here.

The terms “identical” or percent “identity,” in the context of two or more nucleic acids or polypeptide sequences, refer to two or more sequences or subsequences that are the same or have a specified percentage of amino acid residues or nucleotides that are the same, when compared and aligned for maximum correspondence over a comparison window, as measured using one of the following sequence comparison algorithms or by manual alignment and visual inspection. When percentage of sequence identity is used in reference to proteins or peptides, it is recognized that residue positions that are not identical often differ by conservative amino acid substitutions, where amino acids residues are substituted for other amino acid residues with similar chemical properties (e.g., charge or hydrophobicity) and therefore do not change the functional properties of the molecule. Where sequences differ in conservative substitutions, the percent sequence identity may be adjusted upwards to correct for the conservative nature of the substitution. Means for making this adjustment are well known to those of skill in the art. Typically this involves scoring a conservative substitution as a partial rather than a full mismatch, thereby increasing the percentage sequence identity. Thus, for example, where an identical amino acid is given a score of 1 and a non-conservative substitution is given a score of zero, a conservative substitution is given a score between zero and 1. The scoring of conservative substitutions is calculated according to, e.g., the algorithm of Meyers & Miller, Computer Applic. Biol. Sci. 4:11–17 (1988) e.g., as implemented in the program PC/GENE (Intelligenetics, Mountain View, Calif., USA).

The phrase “substantially identical,” in the context of two nucleic acids or polypeptides, refers to sequences or subsequences that have at least 60%, preferably at least about 70% or 80%, most preferably 90 or 95% nucleotide or amino acid residue identity when aligned for maximum correspondence over a comparison window as measured using one of the following sequence comparison algorithms or by manual alignment and visual inspection. This definition also refers to the complement of a test sequence, which has substantial sequence or subsequence complementarity when the test sequence has substantial identity to a reference sequence.

For sequence comparison, typically one sequence acts as a reference sequence, to which test sequences are compared. When using a sequence comparison algorithm, test and reference sequences are entered into a computer, subsequence coordinates are designated, if necessary, and sequence algorithm program parameters are designated. Default program parameters can be used, or alternative parameters can be designated. The sequence comparison algorithm then calculates the percent sequence identities for the test sequences relative to the reference sequence, based on the program parameters.

A “comparison window”, as used herein, includes reference to a segment of any one of the number of contiguous positions selected from the group consisting of from 20 to 600, usually about 50 to about 200, more usually about 100 to about 150 in which a sequence may be compared to a reference sequence of the same number of contiguous positions after the two sequences are optimally aligned. Methods of alignment of sequences for comparison are well-known in the art. Optimal alignment of sequences for comparison can be conducted, e.g., by the local homology algorithm of Smith & Waterman, Adv. Appl. Math. 2:482 (1981), by the homology alignment algorithm of Needleman & Wunsch, J. Mol. Biol. 48:443 (1970), by the search for similarity method of Pearson & Lipman, Proc. Nat'l. Acad. Sci. USA 85:2444 (1988), by computerized implementations of these algorithms (GAP, BESTFIT, FASTA, and TFASTA in the Wisconsin Genetics Software Package, Genetics Computer Group, 575 Science Dr., Madison, Wis.), or by manual alignment and visual inspection.

One example of an algorithm that is suitable for determining percent sequence identity and sequence similarity is the BLAST algorithm, which is described in Altschul et al., J. Mol. Biol. 215:403–410 (1990). Software for performing BLAST analyses is publicly available through the National Center for Biotechnology Information (http://www.ncbi.nlm.nih.gov/). This algorithm involves first identifying high scoring sequence pairs (HSPs) by identifying short words of length W in the query sequence, which either match or satisfy some positive-valued threshold score T when aligned with a word of the same length in a database sequence. T is referred to as the neighborhood word score threshold (Altshul, et al., J. Mol. Biol., 215:403–410 (1990)). These initial neighborhood word hits act as seeds for initiating searches to find longer HSPs containing them. The word hits are extended in both directions along each sequence for as far as the cumulative aligmnent score can be increased. Extension of the word hits in each direction are halted when: the cumulative alignment score falls off by the quantity X from its maximum achieved value; the cumulative score goes to zero or below, due to the accumulation of one or more negative-scoring residue alignments; or the end of either sequence is reached. The BLAST algorithm parameters W, T, and X determine the sensitivity and speed of the alignment. The BLAST program uses as defaults a wordlength (W) of 11, the BLOSUM62 scoring matrix (see Henikoff & Henikoff, Proc. Natl. Acad. Sci. USA 89:10915 (1989)) alignments (B) of 50, expectation (E) of 10, M=5, N=−4, and a comparison of both strands.

The BLAST algorithm also performs a statistical analysis of the similarity between two sequences (see, e.g., Karlin & Altschul, Proc. Nat'l. Acad. Sci. USA 90:5873–5787 (1993)). One measure of similarity provided by the BLAST algorithm is the smallest sum probability (P(N)), which provides an indication of the probability by which a match between two nucleotide or amino acid sequences would occur by chance. For example, a nucleic acid is considered similar to a reference sequence if the smallest sum probability in a comparison of the test nucleic acid to the reference nucleic acid is less than about 0.2, more preferably less than about 0.01, and most preferably less than about 0.001.

Another example of a useful algorithm is PILEUP. PILEUP creates a multiple sequence alignment from a group of related sequences using progressive, pairwise alignments to show relationship and percent sequence identity. It also plots a tree or dendogram showing the clustering relationships used to create the alignment. PILEUP uses a simplification of the progressive alignment method of Feng & Doolittle, J. Mol. Evol. 35:351–360 (1987). The method used is similar to the method described by Higgins & Sharp, CABIOS 5:151–153 (1989). The program can align up to 300 sequences, each of a maximum length of 5,000 nucleotides or amino acids. The multiple alignment procedure begins with the pairwise alignment of the two most similar sequences, producing a cluster of two aligned sequences. This cluster is then aligned to the next most related sequence or cluster of aligned sequences. Two clusters of sequences are aligned by a simple extension of the pairwise alignment of two individual sequences. The final alignment is achieved by a series of progressive, pairwise alignments. The program is run by designating specific sequences and their amino acid or nucleotide coordinates for regions of sequence comparison and by designating the program parameters. For example, a reference sequence can be compared to other test sequences to determine the percent sequence identity relationship using the following parameters: default gap weight (3.00), default gap length weight (0.10), and weighted end gaps.

“Conservatively modified variants” applies to both amino acid and nucleic acid sequences. With respect to particular nucleic acid sequences, conservatively modified variants refers to those nucleic acids which encode identical or essentially identical amino acid sequences, or where the nucleic acid does not encode an amino acid sequence, to essentially identical sequences. Because of the degeneracy of the genetic code, a large number of functionally identical nucleic acids encode any given protein. For instance, the codons GCA, GCC, GCG and GCU all encode the amino acid alanine. Thus, at every position where an alanine is specified by a codon, the codon can be altered to any of the corresponding codons described without altering the encoded polypeptide. Such nucleic acid variations are “silent variations,” which are one species of conservatively modified variations. Every nucleic acid sequence herein which encodes a polypeptide also describes every possible silent variation of the nucleic acid. One of skill will recognize that each codon in a nucleic acid (except AUG, which is ordinarily the only codon for methionine) can be modified to yield a functionally identical molecule. Accordingly, each silent variation of a nucleic acid which encodes a polypeptide is implicit in each described sequence.

As to amino acid sequences, one of skill will recognize that individual substitutions, deletions or additions to a nucleic acid, peptide, polypeptide, or protein sequence which alters, adds or deletes a single amino acid or a small percentage of amino acids in the encoded sequence is a “conservatively modified variant” where the alteration results in the substitution of an amino acid with a chemically similar amino acid. Conservative substitution tables providing functionally similar amino acids are well known in the art. One of skill will recognize, however, that conservative amino acid substitutions may still affect the properties of the protein in terms of polarity, hydrophobicity, enzymatic activity, and the like. Similarly, less conservative amino acid substitutions may have little effect on the properties of the protein, depending, for example, on the region of the protein in which the substitution is made.

The following six groups each contain amino acids that are conservative substitutions for one another:

-   1) Alanine (A), Serine (S), Threonine (T); -   2) Aspartic acid (D), Glutaric acid (E); -   3) Asparagine (N), Glutamine (Q); -   4) Arginine (R), Lysine (K); -   5) Isoleucine (I), Leucine (L), Methionine (M), Valine (V); and -   6) Phenylalanine (F), Tyrosine (Y), Tryptophan (W).     (see, e.g., Creighton, Proteins (1984)).

An indication that two nucleic acid sequences or polypeptides are substantially identical is that the polypeptide encoded by the first nucleic acid is immunologically cross reactive with the antibodies raised against the polypeptide encoded by the second nucleic acid. Thus, a polypeptide is typically substantially identical to a second polypeptide, for example, where the two peptides differ only by conservative substitutions. Another indication that two nucleic acid sequences are substantially identical is that the two molecules or their complements hybridize to each other under stringent conditions, as described below.

The phrase “selectively (or specifically) hybridizes to” refers to the binding, duplexing, or hybridizing of a molecule only to a particular nucleotide sequence under stringent hybridization conditions when that sequence is present in a complex mixture (e.g., total cellular or library DNA or RNA).

The phrase “stringent hybridization conditions” refers to conditions under which a probe will hybridize to its target subsequence, typically in a complex mixture of nucleic acid, but to no other sequences. Stringent conditions are sequence-dependent and will be different in different circumstances. Longer sequences hybridize specifically at higher temperatures. An extensive guide to the hybridization of nucleic acids is found in Tijssen, Techniques in Biochemistry and Molecular Biology—Hybridization with Nucleic Probes, “Overview of principles of hybridization and the strategy of nucleic acid assays” (1993). Generally, highly stringent conditions are selected to be about 5–10° C. lower than the thermal melting point (T_(m)) for the specific sequence at a defined ionic strength pH. Low stringency conditions are generally selected to be about 15–30° C. below the T_(m). The T_(m) is the temperature (under defined ionic strength, pH, and nucleic concentration) at which 50% of the probes complementary to the target hybridize to the target sequence at equilibrium (as the target sequences are present in excess, at T_(m), 50% of the probes are occupied at equilibrium). Stringent conditions will be those in which the salt concentration is less than about 1.0 M sodium ion, typically about 0.01 to 1.0 M sodium ion concentration (or other salts) at pH 7.0 to 8.3 and the temperature is at least about 30° C. for short probes (e.g., 10 to 50 nucleotides) and at least about 60° C. for long probes (e.g., greater than 50 nucleotides). Stringent conditions may also be achieved with the addition of destabilizing agents such as formamide. For selective or specific hybridization, a positive signal is at least two times background, preferably 10 time background hybridization.

Nucleic acids that do not hybridize to each other under stringent conditions are still substantially identical if the polypeptides which they encode are substantially identical. This occurs, for example, when a copy of a nucleic acid is created using the maximum codon degeneracy permitted by the genetic code. In such cased, the nucleic acids typically hybridize under moderately stringent hybridization conditions.

In the present invention, genomic DNA or cDNA comprising nucleic acids useful in the invention can be identified in standard Southern blots under stringent conditions using the nucleic acid sequences disclosed here. For the purposes of this disclosure, suitable stringent conditions for such hybridizations are those which include a hybridization in a buffer of 40% formamide, 1 M NaCl, 1% SDS at 37° C., and at least one wash in 0.2×SSC at a temperature of at least about 50° C., usually about 55° C. to about 60° C., for 20 minutes, or equivalent conditions. A positive hybridization is at least twice background. Those of ordinary skill will readily recognize that alternative hybridization and wash conditions can be utilized to provide conditions of similar stringency.

A further indication that two polynucleotides are substantially identical is if the reference sequence, amplified by a pair of oligonucleotide primers, can then be used as a probe under stringent hybridization conditions to isolate the test sequence from a cDNA or genomic library, or to identify the test sequence in, e.g., a northern or Southern blot.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 shows the catalytic frame of the Fucus vanadium peroxidase.

FIG. 2 shows the organization of the α-helices in the F4R5 active fragment of the invention. Catalytic frame helices are labeled α1–α4, and non-frame helices in intervening loops are indicated as a–d. The location of vanadium-binding amino acid motifs are shown at van1–van3. Deletions at both terminal (T1, T4) and internal (T2, T3) truncation targets further reduce the active vanadium peroxidase in size and promote rapid refolding of solubilized inclusion bodies.

FIG. 3 shows the results of experiments testing the enzymatic activity of truncated enzymes of the invention.

FIG. 4 shows the differences in the F4R5 regions of the Fucus and Ascophyllum haloperoxidase sequences.

FIG. 5 shows motifs conserved among algal and fungal haloperoxidases (SEQ ID NOS:9, 12 and 13, 10, 14–16 and 11, and 17–19, respectively).

DETAILED DESCRIPTION OF THE INVENTION

The practice of this invention involves the construction of recombinant nucleic acids and the expression of genes in transfected host cells. Molecular cloning techniques to achieve these ends are known in the art. A wide variety of cloning and in vitro amplification methods suitable for the construction of recombinant nucleic acids such as expression vectors are well-known to persons of skill. Examples of these techniques and instructions sufficient to direct persons of skill through many cloning exercises are found in Sambrook et al., Molecular Cloning: A Laboratory Manual, 2nd Ed., Vols. 1–3, Cold Spring Harbor Laboratory (1989); Berger and Kimmel, Guide to Molecular Cloning Techniques, Methods in Enzymology volume 152 Academic Press, Inc., San Diego, Calif.; and Current Protocols in Molecular Biology, F. M. Ausubel et al., eds., Current Protocols, a joint venture between Greene Publishing Associates, Inc. and John Wiley & Sons, Inc. (1994 Supplement).

Preparation of Nucleic Acids of the Invention

Nucleic acids encoding vanadium bromoperoxidase polypeptides of this invention can be prepared by any suitable method known in the art, including, for example, cloning and restriction of appropriate sequences or direct chemical synthesis by methods such as the phosphotriester method of Narang et al. (1979) Meth. Enzymol. 68: 90–99; the phosphodiester method of Brown et al. (1979) Meth. Enzymol. 68: 109–151; the diethylphosphoramidite method of Beaucage et al. (1981) Tetra. Lett., 22: 1859–1862; and the solid support method of U.S. Pat. No. 4,458,066.

In one preferred embodiment, the desired nucleic acids encoding a vanadium bromoperoxidase are isolated by routine cloning methods. A nucleotide sequence encoding the enzyme (as provided below, for example) is used to construct probes that specifically hybridize to a bromoperoxidase gene in a genomic DNA sample, or to mRNA in a total RNA sample (e.g., in a Southern or Northern blot). Once the target nucleic acid is identified, it can be isolated according to standard methods known to those of skill in the art.

The desired nucleic acids can also be cloned using well known amplification techniques. Examples of protocols sufficient to direct persons of skill through in vitro amplification methods, including the polymerase chain reaction (PCR) the ligase chain reaction (LCR), Qβ-replicase amplification and other RNA polymerase mediated techniques are found in Berger, Sambrook, and Ausubel, as well as Mullis et al. (1987) U.S. Pat. No. 4,683,202; PCR Protocols A Guide to Methods and Applications (Innis et al. eds) Academic Press Inc. San Diego, Calif. (1990) (Innis); Arnheim & Levinson (Oct. 1, 1990) C&EN 36–47; The Journal Of NIH Research (1991) 3: 81–94; (Kwoh et al. (1989) Proc. Natl. Acad. Sci. USA 86: 1173; Guatelli et al. (1990) Proc. Natl. Acad. Sci. USA 87: 1874; Lomell et al. (1989) J. Clin. Chem. 35: 1826; Landegren et al. (1988) Science 241: 1077–1080; Van Brunt (1990) Biotechnology 8: 291–294; Wu and Wallace (1989) Gene 4: 560; and Barringer et al. (1990) Gene 89: 117. Improved methods of cloning in vitro amplified nucleic acids are described in Wallace et al., U.S. Pat. No. 5,426,039. Suitable primers for use in the amplification of the nucleic acids of the invention are described in the Example Section, below.

The desired nucleic acid can also be cloned by detecting its expressed product by means of assays based on the physical, chemical, or immunological properties of the expressed protein. For example, one can identify a cloned bromoperoxidase nucleic acid by the ability of a polypeptide encoded by the nucleic acid to catalyze the oxidation of o-dianisidine HCl (ODA) as described in the examples below.

In some embodiments, it may be desirable to modify the bromoperoxidase nucleic acids of the invention. One of skill will recognize many ways of generating alterations in a given nucleic acid construct. Such well-known methods include site-directed mutagenesis, PCR amplification using degenerate oligonucleotides, exposure of cells containing the nucleic acid to mutagenic agents or radiation, chemical synthesis of a desired oligonucleotide (e.g., in conjunction with ligation and/or cloning to generate large nucleic acids) and other well-known techniques. See, e.g., Giliman and Smith (1979) Gene 8:81–97, Roberts et al. (1987) Nature 328: 731–734. The modified polypeptides can be tested for activity using the ODA assays described below.

Preparation of Expression Cassettes Encoding Bromoperoxidase Polypeptides of the Invention

The nucleic acid sequences of the invention are incorporated into expression cassettes for high level expression in a desired host cell according to techniques well known to those of skill in the art. The particular host cell used is not critical to the invention and can be either a prokaryotic or eukaryotic cell, as described below.

A typical expression cassette contains a promoter operably linked to the desired DNA sequence. Commonly used prokaryotic control sequences, which are defined herein to include promoters for transcription initiation, optionally with an operator, along with ribosome binding site sequences, include such commonly used promoters as the beta-lactamase (penicillinase) and lactose (lac) promoter systems (Change et al., Nature (1977) 198: 1056), the tryptophan (trp) promoter system (Goeddel et al., Nucleic Acids Res. (1980) 8: 4057), the tac promoter (DeBoer, et al., Proc. Natl. Acad. Sci. U.S.A. (1983) 80:21–25); and the lambda-derived P_(L) promoter and N-gene ribosome binding site (Shimatake et al., Nature (1981) 292: 128). The particular promoter system is not critical to the invention, any available promoter that functions in prokaryotes can be used.

Either constitutive or regulated promoters can be used in the present invention. Regulated promoters can be advantageous because the host cells can be grown to high densities before expression of the bromoperoxidase polypeptides is induced. High level expression of heterologous proteins slows cell growth in some situations. Regulated promoters especially suitable for use in E. coli include the bacteriophage lambda P_(L) promoter, the hybrid trp-lac promoter (Amann et al., Gene (1983) 25: 167; de Boer et al., Proc. Natl. Acad. Sci. USA (1983) 80: 21, and the bacteriophage T7 promoter (Studier et al., J. Mol. Biol. (1986); Tabor et al., (1985). These promoters and their use are discussed in Sambrook et al., supra.

For expression of the polypeptides in prokaryotic cells other than E. coli, a promoter that functions in the particular prokaryotic species is required. Such promoters can be obtained from genes that have been cloned from the species, or heterologous promoters can be used. For example, the hybrid trp-lac promoter functions in Bacillus in addition to E. coli.

A ribosome binding site (RBS) is conveniently included in the expression cassettes of the invention. An RBS in E. coli, for example, consists of a nucleotide sequence 3–9 nucleotides in length located 3–11 nucleotides upstream of the initiation codon (Shine and Dalgarno, Nature (1975) 254: 34; Steitz, In Biological regulation and development: Gene expression (ed. R. F. Goldberger), vol. 1, p. 349, 1979, Plenum Publishing, NY).

Translational coupling may be used to enhance expression. The strategy uses a short upstream open reading frame derived from a highly expressed gene native to the translational system, which is placed downstream of the promoter, and a ribosome binding site followed after a few amino acid codons by a termination codon. Just prior to the termination codon is a second ribosome binding site, and following the termination codon is a start codon for the initiation of translation. The system dissolves secondary structure in the RNA, allowing for the efficient initiation of translation. See Squires, et. al. (1988), J. Biol. Chem. 263: 16297–16302.

The polypeptides can be expressed intracellularly, or can be secreted from the cell. Intracellular expression often results in high yields. If necessary, the amount of soluble, active polypeptide may be increased by performing refolding procedures (see, e.g., Sambrook et al., supra.; Marston et al., Bio/Technology (1984) 2: 800; Schoner et al., Bio/Technology (1985) 3: 151).

In embodiments in which the bromoperoxidase polypeptides are secreted from the cell, either into the periplasm or into the extracellular medium, the DNA sequence is linked to a cleavable signal peptide sequence. The signal sequence directs translocation of the bromoperoxidase polypeptide through the cell membrane. An example of a suitable vector for use in E. coli that contains a promoter-signal sequence unit is pTA1529, which has the E. coli phoA promoter and signal sequence (see, e.g., Sambrook et al., supra.; Oka et al., Proc. Natl. Acad. Sci. USA 82: 7212 (1985); Talmadge et al., Proc. Natl. Acad. Sci. USA, 77:3988 (1980); Takahara et al., J. Biol. Chem., 260:2670 (1985)).

One of skill would recognize that other modifications can be made to the bromoperoxidase polypeptides without diminishing their biological activity. Modifications may be made to improve various properties of the enzyme or to facilitate the cloning, expression, and the like. For example, the minimal catalytic frame helices disclosed here can be modified to have different surface properties and thereby increase frame stability. Such modifications are discussed in more detail below. Modifications to enhance cloning and expression are well known to those of skill in the art and include, for example, a methionine added at the amino terminus to provide an initiation site, or additional amino acids that form an purification tag (e.g., poly His) placed on either terminus to facilitate purification. In addition, one of skill will recognize that fusion proteins with various heterologous protein sequences can be prepared. For example, overexpression of a protein can lead to the accumulation of folding intermediates which have a tendency to aggregate. Production of fusion proteins including sequences, such as bacterial thioredoxin, can be used to facilitate proper folding. The polypeptides of the invention can also be fused to other proteins to allow quantification or localization of the linked protein. Thus, the fusion partner can be detected by the presence of the peroxidase activity of the enzyme of the invention. The fusion partner may also be a bacterial protein that results in increased yields, because normal prokaryotic control sequences direct transcription and translation. In E. coli, lacZ fusions are often used to express heterologous proteins. Suitable vectors are readily available, such as the pUR, pEX, and pMR100 series (see, e.g., Sambrook et al., supra.).

For certain applications, it may be desirable to cleave the non-bromoperoxidase amino acids from the fusion protein after purification. This can be accomplished by any of several methods known in the art, including cleavage by cyanogen bromide, a protease (e.g., enterokinase), or by Factor X_(a), (see, e.g., Sambrook et al., supra.; Itakura et al., Science (1977) 198: 1056; Goeddel et al., Proc. Natl. Acad. Sci. USA (1979) 76: 106; Nagai et al., Nature (1984) 309: 810; Sung et al., Proc. Natl. Acad. Sci. USA (1986) 83: 561). Cleavage sites can be engineered into the gene for the fusion protein at the desired point of cleavage.

A suitable system for obtaining recombinant proteins from E. coli which maintains the integrity of their N-termini has been described by Miller et al. Biotechnology 7:698–704 (1989). In this system, the gene of interest is produced as a C-terminal fusion to the first 76 residues of the yeast ubiquitin gene containing a peptidase cleavage site. Cleavage at the junction of the two moieties results in production of a protein having an intact authentic N-terminal reside.

Expression of Bromoperoxidase Polypeptides of the Invention

Bromoperoxidases of the invention can be expressed in a variety of host cells, including E. coli, other bacterial hosts, yeast, and various higher eukaryotic cells such as algal cells. For example microalgal expression systems, useful in the invention include the diatom Phaeodactylum tricornutum (Apt et al. J. Phycol. 32:4 (1996)).

Examples of useful bacteria include, but are not limited to, Escherichia, Enterobacter, Azotobacter, Erwinia, Bacillus, Pseudomonas, Klebsielia, Proteus, Salmonella, Serratia, Shigella, Rhizobia, Vitreoscilla, and Paracoccus. The recombinant protein gene will be operably linked to appropriate expression control sequences for each host. For E. coli this includes a promoter such as the T7, trp, or lambda promoters, a ribosome binding site and preferably a transcription termination signal. For eukaryotic cells, the control sequences will include a promoter and preferably an enhancer derived from immunoglobulin genes, SV40, cytomegalovirus, etc., and a polyadenylation sequence, and may include splice donor and acceptor sequences.

The expression vectors of the invention can be transferred into the chosen host cell by well-known methods such as calcium chloride transformation for E. coli and calcium phosphate treatment or electroporation for mammalian cells. Cells transformed by the plasmids can be selected by resistance to antibiotics conferred by genes contained on the plasmids, such as the amp, gpt, neo and hyg genes.

Once expressed, the recombinant bromoperoxidase polypeptides can be purified according to standard procedures of the art, including ammonium sulfate precipitation, affinity columns, column chromatography, gel electrophoresis and the like (see, generally, R. Scopes, Protein Purification, Springer-Verlag, N.Y. (1982), Deutscher, Methods in Enzymology Vol. 182: Guide to Protein Purification., Academic Press, Inc. N.Y. (1990)). Substantially pure compositions of at least about 90 to 95% homogeneity are preferred, and 98 to 99% or more homogeneity are most preferred. Once purified, partially or to homogeneity as desired, the polypeptides may then be used (e.g., as immunogens for antibody production).

When the proteins of the invention are expressed in bacteria, large amounts of the expressed protein is present in inclusion bodies. The wet weight of inclusion bodies produced is in the range of 1–4 mg/mL of bacterial culture, constituting up to 40% of total cell protein (Novagen). Following standard washing procedures, the inclusion bodies contain expressed protein up to 95% in purity. A preferred method of purifying the enzymes from inclusion bodies is to wash the protein from inclusion bodies and use a simple one step refolding procedure. One such method is to solublize the protein in alkali at pH 10–12 (e.g., with NaOH, KOH, Caps). The protein is then refolded in ammonium sulfate (preferably at pH 5.6 to 8.0)±minimolar levels of magnesium chloride at room temperature. Alternatively the protein can be refolded in magnesium sulfate up to about 0.5 M (pH 5.6–8.0) at between about 0° C. to about 10° C. The protein can also be refolded in imidazole and either sodium or potassium chloride, preferably at pH7–8 and preferably at 10–17° C., which is the temperature of the seawater in which the marine algae grow. Detergents such as Tween-20, BPer (Pierce Chemical Company) or BugBuster (Novagen) are optional in all three refolding procedures.

The purified haloperoxidase polypeptides of the invention can be used in a number of industrial applications. The polypeptides can be used for any purpose to which prior art haloperoxidases are used. For instance, the polypeptides can be used to halogenate various substrates, including proteins. For instance the polypeptides can be used to produce epoxides from alkenes, halogenated ketones from alkynes, to produce alpha, gamma-halohydrins from cyclopropanes, and to produce dihalogenated products from alkenes and alkynes. In addition, the ability of the polypeptides to oxidize various compounds make them useful, for instance, in signal generating systems in place of horseradish peroxidase. Thus, the haloperoxidase polypeptides of the invention can be used as a component in assays as described in WO 97/09619. The polypeptides can also be as enzymatic antimicrobial agents (see, e.g., WO 95/27046). Other uses include production of phenolic adhesives as described in U.S. Pat. No. 5,520,727.

Modified Haloperoxidase Polypeptides

Based on the results provided here, one of skill can readily construct and test a number modified haloperoxidases from brown algae, red algae (e.g., Corallina) and fungi (e.g., Curvularia). These modified enzymes can be designed using methods well known in the art for introducing modifications (e.g., substitutions, additions, and deletions) can be made to provide enhanced activity, stability, or to facilitate proper refolding, purification, and the like, as desired. These modified proteins can be tested for the desired properties using assays disclosed here.

As demonstrated below, the entire catalytic domain of the haloperoxidase enzymes is not necessary for catalytic activity (see, Example 2). The basic organization of haloperoxidase enzymes is a catalytic helical frame found at the core of the monomeric unit. In Fucus the helical frame is an M-shape or zig-zag with the vanadate-bound active site at the top of the “M” (see, FIG. 1). The helices forming the helical frame correspond to amino acids 439–631 of SEQ D NO: 1. The catalytic frame helices (CFH) 1-2-3-4 (see, Table 3) correspond to helices K-O-Q-R, respectively in the Ascophyllum enzyme X-ray structure as reported by Weyland et al. (1999). A protein fold to similar to the catalytic helical frame in the core of the brown algal enzymes is seen in the separate catalytic domain of the fungal enzymes (Barnett et al. J Biol Chem 273, 23381–7 (1998), although there is no homology between the Ascophyllum and fungal enzymes except at the conserved vanadate binding motifs. Differences in these folds include the length and helical content of the variable loop between the first and second vanadate binding sites, an elongated loop following the third vanadate binding site only for the fungal enzymes, and the presence of additional helices in the fungal catalytic domain. From site mutation studies on several vanadate binding amino acids in a fungal active site, Macedo-Ribeiro et al. J Biol Inorg Chem 4:209–19 (1999) concluded that the many hydrogen bonding and salt bridge interactions at the catalytic site of the fungal enzyme formed a very rigid matrix or frame for oxyanion binding.

Active truncated enzymes which consist of the catalytic frame helices of a particular enzyme can be prepared. In addition, the simple antiparallel helical motif can refold more easily when the loops which separate the frame helices are shortened. In the case of Fucus, the first two of the three helical intersections along the M-shaped bundle (between helices 1–2 and 2–3) can be minimized (see FIG. 2). These loops form gaps of 74 amino acids between helices 1 and 2 and 31 amino acids between helices 2 and 3 (in contrast to 4 amino acids between helices 3 and 4). As noted above, when the protein is expressed in bacterial cells, most of the expressed protein is in inclusion bodies. Shortening the loops greatly facilitates correct protein refolding from the inclusion bodies. Such modifications also change the protein surface properties, since the surface loops are both acidic. The isoelectric point changes from acidic (pI 5.5) to basic (pI 8.7–9.2) when both loops are minimized.

The removal of the helix 1–2 acidic surface loop covering the catalytic site situates the catalytic site on the surface of the recombinant enzyme, held in place by the rigid helical frame, instead of being buried deep in a narrow, funnel-shaped cavity as in the native enzyme. Greater access to the catalytic site has two important consequences: the enzymatic turnover rate increases and additional and larger substrates can be accommodated. The size of the minimal active helical frame will be in the 9–10 kDa range after maximal terminal and internal truncation.

Analysis of amino acid differences between the Fucus and Ascophyllum enzymes, especially in the catalytic bundle and conserved sites, can be used to design enzymes with improved properties. As shown in FIG. 4 and Table 1, of the twenty-one amino acid differences between the Fucus and Ascophyllum enzymes in the F4R5 region, three are near the first and second vanadium-binding amino acids and are likely to be involved in the several-fold greater activity of the Fucus enzyme. These three sites are Ala 455, Cys 457 and Val 525. As noted above, the Fucus enzyme is more active than the Acophyllum and other algal and fungal enzymes. Thus, haloperoxidase enzymes can be engineered to include one or more of the 21 unique amino acids from the Fucus sequence to improve the properties of a particular enzyme. To do this the corresponding amino acid residues in a second haloperoxidase (e.g., the Ascophyllum enzyme) are identified by comparison of the amino acid sequence as well as the secondary, tertiary and quaternary structure of the proteins (e.g., using X ray crystallography and other well known techniques) to identify those residues that correspond to the residues identified in Table 1. The three short conserved vanadate binding motifs, which can readily be recognized by sequence alignment, are shown in FIG. 5. They are always present in the same order, and include the algal bromoperoxidases, the fungal chloroperoxidases, and some groups of phosphatases (Hemrika et al., Proc. Natl. Acad. Sci. U.S.A. 94:2145–2149 (1997); Stukey and Carman Protein Science 6:469–72 (1997). The identified amino acid residues are then substituted with the corresponding Fucus residue. Alternatively, the catalytic helical frame can be modified to more closely approximate the geometry of the Fucus active site. The geometry at the vanadium haloperoxidase active site differed between Ascophyllum and Curvularia enzymes (see Weyland et al. 1999 and Wever et al. 1997), Curvularia single site mutants (see Macedo-Ribeiro et al. 1999) and among the three fungal enzymes (Barnett et al. 1998). The Fucus and Ascophyllum vanadium binding sites are very similar in primary sequence, except as noted in Table 1. The geometry of the catalytic site of the Fucus enzyme is clearly unique as demonstrated by its severalfold greater activity than other vanadium haloperoxidases. The modified enzymes can be readily tested for activity and other properties according to standard techniques.

TABLE 1 Fucus/Asco. Equivalent RVP × 1 Amino acid Ascophyllum Number Fucus Site Location Differences Site  1 Thr439 α1 helix Polar/Hydrophobic Ile320  2 Ala455 1^(st) van. Hydrophobic/Polar Ser336 Bind.  3 Cys457 1^(st) van. Small/Large Trp338 Bind.  4 Asn478 α1–α2 loop Polar/Hydrophobic Leu359  5 Ala481 α1–α2 loop Hydrophobic/Basic Lys362  6 Asp483 α1–α2 loop Acidic/Acidic Glu364  7 Asp485 α1–α2 loop Acidic/Polar Asn366  8 Ile490 α1–α2 loop Both Hydrophobic Leu371  9 Asp496 α1–α2 loop Acidic/Hydrophobic Ala377 10 Glu504 α1–α2 loop Acid/Hydrophobic Ala385 11 Val525 2^(nd) van. Hydrophobic/Acidic Glu406 bind. 12 Glu559 α3–α4 loop Both Acidic Asp440 13 Phe561 α3–α4 loop Hydrophobic Polar Tyr442 14 Asn563 α3–α4 loop Polar/Acidic Asp444 15 Phe566 α3–α4 loop Hydrophobic/Polar Tyr447 16 Ser568 α3–α4 loop Hydrophobic/Acidic Asp449 17 Glu573 α3–α4 loop Acidic/Basic Lys454 18 Asn576 α3–α4 loop Polar/Acidic Asp457 19 Glu578 α3–α4 loop Acidic/Basic Arg459 20 Ala580 α3–α4 loop Hydrophobic/Polar Ser461 21 Tyr584 α3 helix Polar/Hydrophobic Phe465

EXAMPLE 1

This example describes the cloning of a vanadium bromoperoxidase gene of the invention.

Materials and Methods

DNA library. A Fucus distichus 2-cell embryos c-DNA library was prepared the λ-ZipLoxL1 plasmid (Gibco BRL, Gaithersburg, Md.) and is described in Goodner, et at., Plant Physiology, 107:1007–1008 (1995).

Antibody screening. An antibody to Corallina vancouverensis vanadium peroxidase was prepared which identified Fucus distichus vanadium peroxidase on Western blots of crude extracts.

DNA Hybridization Method. Hybridization probes were prepared at the second and near the third regions shown to be conserved between Curvularia and Ascophyllum vanadium peroxidase active sites by Messerschmidt, et al., PNAS, 93:392–396 (1996). Hybridization probes of 51 base pairs were designed with Oligo 5.0 Primer Analysis Software (National Biochemicals, Plymouth, Minn.), synthesized by Anagen (Palo Alto), and digoxigenin-labeled at the 5′ end with the Genius system (BMB Biochemicals, Durham, N.C.). The sequence of the probe for the second conserved site was:

-   -   CCAACGCACCCTTCGTACCCGTCTGGCCACGCTACCCAAAACGGAGCATTT.         The sequence of the probe for the third conserved site was:     -   CCGTACGAACACTTCACCAGGAGCTGATGACTTTCGCCGAGGAATCCACCT.

Sequencing. Sequencing of the Fucus vanadium peroxidase clone was accomplished by primer walking. M13 universal primers and primers designed from Fucus and Ascophyllum Vanadium haloperoxidase sequences with Oligo software and synthesized by Operon (Alameda, Calif.). ABI dye-terminator sequencing was done by the UCB Molecular and Cellular Biology DNA Sequencing Facility in Barker Hall.

Homology. DNA and protein searches on databases accessible online through GenBank using the BLAST algorithm (Altshul, et al., J. Mol. Biol., 215:403–410 (1990)).

Protein Expression In order to optimize correct folding for peroxidase activity, recombinant Fucus vanadium peroxidase constructs were prepared and expressed in E. coli as fusion proteins with thioredoxin at the N-terminal end (pET-32 LIC Ligation Independent Cloning vector, Novagen, Madison, Wis.). This vector produces a high level of expression of soluble recombinant proteins in E. coli cytoplasm. While note necessary, the expressed protein can be fused with an N-terminal thioredoxin for optimizing correct protein folding, detection and purification, respectively (Novagen). In addition, an enterokinase (EK) cleavage site is located at the N-terminal end of the inserted protein so that native protein can be cleaved from the 19 kDa tagged peptide following expression. Three sizes of constructs were prepared for confirmation of the active site domain at the 3′ end, as suggested by the minimal fungal-Ascophyllum homology reported at the active site (Messerschmidt, et al., PNAS, 93:392–396 (1996)). Expression constructs were prepared for the full length Fucus bromoperoxidase and two 5′-truncated forms (Table 2), corresponding to 100%, 80% and 54% of the full length sequence, respectively. The cloned λ-ZipLox plasmid containing the Fucus vanadium bromoperoxidase cDNA was used as the template for PCR amplification with Vent DNA polymerase (New England Biolabs, Beverly, Mass.).

TABLE 2 Starting point Expressed Construct (bp #) on SEQ VPx bp kDa of Vpx fusion protein Designation ID NO: 1 expressed sequence size in kDa rVP × 1  1 2028 73.5 93 rVP × 2 409 1620 57.7 77 rVP × 3 937 1092 39.6 59

The following Fucus peroxidase LIC primers were designed with Oligo software (National Biosciences, Inc., Plymouth, Minn.) and pET-32 LIC sequences necessary for incorporation into the vector. Primers for the 5′ end were: GACGACGACAAGATGCTTTGCCATGCAGCGGACA (SEQ ID NO:5) (34 bp) for the full length construct, GACGACGACAAGATGGCGCCGAATAGAAGGGACAA (SEQ ID NO:6) (35 bp) for the mid length construct, and GACGACGACAAGATGCTCTTCCGAGCGACCTTC (SEQ ID NO:7) (33 bp) for the short construct. One 3′-primer, GAGGAGAAGCCCGGTTGCACTAAGCCTGGCAGT (SEQ ID NO:8) (33 bp) was used for all three constructs. PCR was carried out for 30 cycles of 3 mm at 940, 1.5 mm at 55° C. and 2.3 mm at 72° C., in 7 mM MgSO4 for the full length construct and 4 mM MgSO4 for the two truncated constructs. The PCR products were electrophoresed in 1.5% agarose and stained with ethidium bromide. DNA was extracted from the excised bands in GenElute minus EtBr spincolumns (Supelco, Bellefonte, Pa.) and precipitated with ethanol.

Ligation independent cloning was carried out according to the pET-32 LIC protocol (Novagen), with a T4 DNA ligase (GibcoBRL, Grand Island, N.Y.) step added prior to transformation for the full length construct. The recombinant plasmids were transformed into the NovaBlue strain of E. coli according to the Novagen protocol. In all bacterial strains transformed, plasmid clones containing peroxidase inserts were identified by PCR of partial Fucus peroxidase sequences with Taq polymerase (Promega, Madison, Wis.) in 1.6–3.75 mM MgCl2 for 30 cycles of 3 min at 94°, 1.5 min at 45° and 2 min at 72°, followed by agarose electrophoresis. Plasmids cloned from NovaBlue cells were expressed in BL21(DE3), BL21(DE3) pLysS and AD494(DE3) E. coli cells (Novagen). The AD494strain is deficient in thioredoxin reductase, which results in an appropriate redox potential for correct folding of eukaryotic proteins (Novagen). Induced bacterial cytoplasmic protein preparations were examined by protein electrophoresis, and the products were tested for vanadium-dependent peroxidase activity. Proteins were expressed for 0, 0.5, 1.5 and 3 h after induction of protein synthesis with IPTG (isopropylthio-b-galactoside). Bacterial lysates were prepared immediately after protein expression.

The recombinant bromoperoxidase proteins were immediately purified from bacterial cytoplasmic proteins by affinity chromatography. The HisTag (a sequence of 6 histidines, 6×His) in the fusion protein was bound to a nickel nitriloacetic acid (Ni+2-NTA) agarose column (Sigma, St. Louis, Mo.) according to the standard Qiagen protocol. The bound recombinant protein containing 6×His was eluted with 1M imidizole in 20 mM Tris-HCl pH 7.9 and 500 mM NaCl. Denatured protein samples were electrophoresed in 8% polyacrylamide gels containing 4% SDS, fixed and stained with Coomassie Brilliant Blue R250. The recombinant vanadium peroxidases (rVPx) were tested for vanadium-dependent peroxidase activity on dot blots. A preliminary in vitro expression experiment was carried out for the three LIC constructs in a bacteriophage transcription system linked with a rabbit reticulocyte translation system (Single Tube Protein System 2, T7, Novagen), and the products were tested for vanadium-dependent peroxidase activity on dot blots.

Vanadium peroxidase activity assay. Peroxidase activity with ODA (o-dianisidine HCl, Sigma) as the substrate was detected by dot blotting 1 μL of enzyme solution onto positively charged nylon membranes (Biodyne B, Pall Corp., Port Washington, N.Y.). Substrate solution contained 100 mM Tris-HCl, pH 8.0, 10 mM KBr, 0.25 mM urea-H2O2, and 1 mM ODA (Sigma). Quantitites of dry KBr, urea-H₂O₂ and ODA were estimated for daily substrate solutions.

RVPx were rapidly revanadated with trace levels of vanadium. 1 μL of 100 mM sodium orthovanadate in a 2 μL pipettor tip was ejected from the tip. The “vanadated” empty tip was then inserted into a 5–10 μL drop of enzyme solution on a piece of Parafilm (Fisher, Hayward, Calif.) and pipetted in and out 5 times. After waiting 1–5 min, 1 μL of the revanadated rVPx was pipetted onto the nylon membrane and air dried for a few minutes. While strong peroxidase activity was visible in a few minutes, the membrane was incubated in the ODA solution overnight.

Antibody labeling on Membranes (Plaque Lifts, Dot Blots and Western Blots). The membranes were blocked overnight at 4° C. in 100 mM Tris-HCl pH 8.0+4% skim milk+0.1% tween-20 and then incubated for 3 h at 37° C. in mouse ascites antibody to Corallina vanadium peroxidase or mouse ascites control antibody (Sigma) diluted 1:1,000 in blocking solution. The blots were washed 3× in blocking solution and incubated in alkaline phosphatase-conjugated anti-mouse second antibody (diluted 1:5,000) for 1 h at room temperature. They were then washed 3× in blocking solution and rinsed in alkaline buffer (100 mM NaCl+100 mM Tris-HCl at pH 9.5.+50 mM MgCl2). Chemiluminescence was detected by of CPD-Star (BMB, Durham, N.C.) (diluted 1: in alkaline buffer) and exposed to X-ray film (Kodak) for 2 h. Alternative colorigenic detection was by overnight incubation in NBT/BCIP substrate (Pierce, Rockford, Ill.).

Results

Fucus cDNA library Screening. The fusion protein for the VPx clone which was expressed during cDNA screening was apparently truncated prior to the VPx start codon, at a TGA stop codon located at bases 82–84 in the 5′ UTR. This truncation upstream of the VPx coding sequence caused a lack of VPx protein expression during screening, explaining the lack of a-VPx antibody labeling during extensive screening. Therefore, two 51 bp DNA probes based on two small regions of homology at the active site between Curvularia chloroperoxidase and Ascophyllum bromoperoxidase (Messerschmidt, et al., PNAS, 93:392–396 (1996)) were used to screen the Fucus embryo cDNA library. Only one clone was identified which was labeled with both of the VPx DNA probes after extensive screening. This clone was about 3 kb in size after Not I/Sal I excision from the plasmid.

Fucus vanadium peroxidase sequence. The sequence of the VPX from 2-cell Fucus gardneri embryos is shown in SEQ ID NO:1 (see, also Genbank Accession No. AF053411). The 2931 base pairs in the Fucus cDNA clone includes 227 bases in the 5′ UTR, 2031 bases in the coding region and 673 bases in the 3′ UTR. The 5′ UTR is a partial sequence, and the 3′ UTR is complete. Translation of the VPx coding sequence produces a 73,353 Da protein containing 676 amino acids. No obvious leader peptide sequence was detected although VPx is secreted (Vreeland, et al., Molecular Biology of the Cell 7 (Supplement), 304a (1996)).

A 73.4 kDa Fucus monomer would be the largest known VPx monomer, although the molecular mass of the native Fucus enzyme is unknown. The 73.4 kDa size is larger than the 60 kDa VPx monomer from a related brown alga, Ascophyllum nodosum, as well as larger than the 67.5 kDa fungal Curvularia inaequalis chloroperoxidase monomer (Simons, et al., European Journal of Biochemistry, 229:566–574 (1995)). The Fucus VPx monomer comigrated with the monomer of the red alga Corallina vancouverensis on PAGE gels (Vreeland, et al., Molecular Biology of the Cell 7 (Supplement), 304a (1996)). The C. officinalis and C. pilulifera VPx monomers are approximately 64 kDa based on SDS PAGE data (Itoh, et al., J. Biological Chemistry 261:5194–5200 (1986); Sheffield, et al., Phytochemistry, 32:21–26 (1993); Rush, et al., FEBS Letters, 359:244–246 (1995)), and the Fucus VPx monomer might therefore be expected to be a similar size. However, the related Fucus and Ascophyllum brown algal VPx monomer sizes differ, and it is also possible that the C. vancouverensis monomer size may differ from the published C. officinalis and C. pilulifera monomer size.

Alternative explanations include utilization of the third start codon in the Fucus VPx sequence to produce a 64,471 Da protein of 596 amino acids. Utilization of the third start codon is supported by the lack of a TATA box upstream of the first two start codons, and the presence of a TATA box 79 bp upstream of the third in-frame ATG. Also possible are different protein shape and/or charge properties resulting in electrophoretic comigration of Fucus and C. vancouverensis monomers.

The Fucus and C. vancouverensis multimers also comigrated, implying that the Fucus multimer may be a dodecamer (Vreeland, et al., Molecular Biology of the Cell 7 (Supplement), 304a (1996)) although the Ascophyllum multimer is a dimer (Vilter 1995), since the C. officinalis and C. pilulifera multimers appear to be dodecamers (Sheffield, et al., Phytochemistry, 32:21–26 (1993); Rush, et al. FEBS Letters, 359:244–246 (1995); Itoh, et al., J. Biological Chemistry 261:5194–5200 (1986)). Although the C-terminal catalytic domain appears to be similar in Fucus and Ascophyllum VPx, their self-associating domains are likely to differ due to their different monomer sizes. The Fucus VPx may contain more than one self-associating domain if it contains the double hexameric ring arrangement as found for the C. pilulifera VPx by Itoh, et al., J. Biological Chemistry 261:5194–5200 (1986), and this may partially account for the larger size of the Fucus VPx in the N-terminal region.

The Fucus and Ascophyllum brown algal VPx were 87.2% identical for 709 base pairs of DNA and 85.8% identical for 232 amino acids for the published partial C-terminal VPx sequence of Ascophyllum (Vilter 1995) when calculated from the best match of the Fucus data with the published Ascophyllum peptide and translated sequences. The amino acid sequence of the revised and completed Ascophyllum enzyme (Weyland et al. 1999) is 89% identical to the Fucus enzyme, and the Fucus enzyme is 123 amino acids longer at the N-terminus and one amino acid longer at the C-terminus.

The Fucus sequence contains three conserved vanadium-binding regions (Messerschmidt et al.). The three conserved vanadium-binding regions are as follows: (1) amino acids 452–473 AQRASCYQKWQVHRFARPEALG; (2) amino acids 528–546 PTHPSYPSGHATQNGAFAT and (3) amino acids 591–609 NKLAVNVAFGRQMLGIHYRFD. In the three conserved vanadium-binding regions the Fucus and Ascophyllum amino acid sequences differ only at two locations in the first conserved region (alanine at Fucus 455 substituted for serine at Ascophyllum 19, and cysteine at Fucus 457 substituted for tryptophan at Ascophyllum 21). These two amino acid differences are therefore likely to be related to the greater specific activity of the Fucus enzyme, as are other amino acid sequence differences in the catalytic frame (amino acids Fucus 441–636). A major difference between the Fucus, Ascophyllum and Corallina algal bromoperoxidases and the fungal chloroperoxidases and various phosphatases is the additional basic amino acids in the first conserved domain of the bromoperoxidases, histidine at Fucus 464 and leucine at Fucus 472 for the brown algal enzymes, with threonine instead of leucine for the Corallina enzyme. These additional amino acids in the first conserved region are likely to be related to the greater activity of the bromoperoxidases with bromide, which is larger than the chloride ion.

Bacterial expression of Fucus vanadium peroxidase constructs. The three recombinant Fucus VPx proteins (rVPx, Table 1) were expressed as soluble cytoplasmic proteins in both BL21(DES) and AD494 strains of E. coli at the expected sizes of recombinant proteins. All of the recombinant proteins were seen as major bands against the background of bacterial proteins. This represents production of about 1–10 mg/100 mL of recombinant proteins, as estimated from the intensity of Coomassie blue-stained bands.

After Ni-NTA column purification, peroxidase activity for rVPx expressed by AD494 cells was tested on dot blots with 0-dianisidine as substrate. No peroxidase activity was detected in the absence of added vanadium, although E. coli contains an 80 kDa o-dianisidine-reactive peroxidase. This result with an extremely sensitive activity assay also demonstrates that the single affinity purification step removed significant contamination by bacterial proteins.

Peroxidase activity was detected in all three rVPx constructs immediately following protein expression and purification, but only in the presence of added vanadium. The activity was relatively weak, and decreased with smaller rVPx construct size. However, after overnight treatment at −20° C., activity was much stronger and of similar intensity for all three construct sizes. Like native algal VPx, the recombinant forms bound to positively charged nylon membranes but did not bind to nitrocellulose membranes. However, the recombinant forms did not bind as tightly to nylon membranes.

The three sizes of rVPx were also expressed in an in vitro rabbit reticulocyte system. It was clear that expression of all three sizes of rVPx occurred, although background peroxidase activity was seen in this eukaryotic system.

Discussion

ODA is a common substrate for heme peroxidases such as horseradish peroxidase and other peroxidases. The product of ODA oxidation by algal vanadium peroxidase was not halogenated, although it is not known whether ODA oxidation by rVPx involves a halogenated intermediate or singlet O2 production. The expression of active rVPx in E. coli demonstrates that glycosylation is not necessary for enzyme activity, and, indeed, the native enzyme is probably not glycosylated. Activity of recombinant enzyme shows that it can be folded correctly in bacterial cytoplasm, as well.

EXAMPLE 2

This example describes identification of the minimal catalytic unit of the enzymes of the invention.

As noted above, the X-ray structure of fungal and algal vanadium peroxidases have been reported Messerschmidt and Wever, (1996), Weyand et al., (1999) and Littlechild, (1999), supra). The algal catalytic helical bundle is found at the core of the monomeric unit, and a more loosely-organized region is found on the side of the core bundle near the catalytic site and away from the dimerization site. According to the Ascophyllum X-ray structure, this outer region consists of helices D, E, F, and H (from the N-terminal half of the protein) which are associated with helices L, M and N (forming a surface loop derived from the middle of the catalytic core bundle of the C-terminal catalytic unit).

The basic organization of the helical frame of the Fucus enzyme is an M-shape or zig-zag with the vanadate-bound active site at the top of the “M” (see, FIG. 1). The helices forming the helical frame and correspond to amino acids 439–631 of SEQ ID NO: 1. FIG. 2 and Table 3 show the catalytic frame helices (CFH) and helices included in the intervening loops. These helices were identified by comparison with Curvularia and Ascophyllum haloperoxidase X-ray structures and with the PepTools protein prediction program (Bio Tools, Inc.). CFH 1–2–3–4 correspond to helices K-O-Q-R, respectively, for the Ascophyllum enzyme X-ray structure as reported by Weyland et al. (1999).

TABLE 3 Homologous Amino Length in Ascophyllum CFH α-Helix Acid Location Amino Acids α-Helix 1 Thr439-Trp461 23 K  a* Pro469-Ala481 13 L  b* Ile490-Leu493  4 M  c* Asp496-Gln509 14 N 2 Gly536-Ile552 17 O  d** Leu554-Gly557  4 P 3 Try584-Leu602 19 Q 4 Arg607-Thr631 25 R *helices in the CFH α1–α2 loop **helix in the CFH α2–α3 loop

Further analysis of the Fucus enzyme revealed that the entire catalytic domain is not necessary for catalytic activity. A number of truncated enzymes were prepared and tested using the assays described in Example 1. The results are presented in FIG. 3. These experiments revealed that the only part needed for vanadium-dependent catalytic activity is the actual catalytic helical bundle. Active enzyme fragments consisting of only the 198 amino acids of the sequence between the 1–4 helices were found (e.g., fragment F4R5 in FIG. 2). Further N- and C-terminal truncation can also be made. In particular, the exposed ends of the 1 and 4 helices are involved in dimerization, and can be shortened, for an additional size reduction to 19.2 kDa while retaining catalytic activity.

The above examples are provided to illustrate the invention but not to limit its scope. Other variants of the invention will be readily apparent to one of ordinary skill in the art and are encompassed by the appended claims. All publications, GenBank Accession references (sequences), patents and patent applications cited herein are hereby expressly incorporated by reference for all purposes. 

1. An isolated polypeptide comprising a vanadium haloperoxidase polypeptide consisting of a catalytic domain that complexes a vanadium ion and catalyzes the oxidation of o-dianisidine (ODA), wherein the vanadium haloperoxidase polypeptide comprises an amino acid sequence having at least 90% sequence identity to the sequence from residue 435 to residue 632 of SEQ ID NO:2, and has a molecular weight of no more than 40 kDa.
 2. The isolated polypeptide of claim 1, wherein the polypeptide comprises an Ala residue at a position corresponding to position 455 of SEQ ID NO: 2, a Cys residue at a position corresponding to position 457 of SEQ ID NO: 2, and a Val residue at position 525 of SEQ ID NO:
 2. 3. The isolated polypeptide of claim 1, wherein the polypeptide has at least 95% identity to a polypeptide as set forth in SEQ ID NO:2.
 4. The isolated polypeptide of claim 1, wherein the amino acid sequence is residue 435 to residue 632 of SEQ ID NO:2.
 5. The isolated polypeptide of claim 1, wherein the polypeptide has a molecular weight of about 20 kDa.
 6. The isolated polypeptide of claim 1, wherein the polypeptide is immobilized on a solid surface.
 7. The isolated polypeptide of claim 1, wherein the polypeptide further comprises a cleavable linker sequence.
 8. The isolated polypeptide of claim 7, wherein the cleavable linker sequence is an enterokinase cleavable linker sequence.
 9. The isolated polypeptide of claim 1, wherein the polypeptide further comprises an purification tag.
 10. The isolated polypeptide of claim 9, wherein the purification tag comprises a plurality of histidine residues. 